Additional file 1:

Neighboring residues of the tryptophans in tCWCH2 3D structure. (A) Distances of the tCWCH2-forming residues from the tCWCH2 ZF1 tryptophan (left) and the tCWCH2 ZF2 tryptophan (right). Black and red letters indicate residues in the ZF1 and the ZF2 respectively. Gothic letters, zinc chelating residue; *, ϕ1 and ϕ2 in Figure 5 and 6. Note that both tryptophan residues were close to the residues in the other C2H2 ZF unit. (B) Stereo view of the ZIC3, GLI1, and Zap1 tryptophan side chain adjacent residues within 5 Å. Tryptophan residues, zinc chelating histidine, ϕ1, and ϕ2 residues are labeled. For ZIC3 and Zap1, 20 NMR models in wire model are superimposed. For GLI1, cylinder model are shown. White, carbon; red, oxygen; blue, nitrogen; yellow; sulfur.

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Additional file 2:

List of tandem CWCH2-containing genes. Gene ID of NCBI or Ensembl http://www.ensembl.org/ webcite or JGI Lottia gigantea genome http://genome.jgi-psf.org/Lotgi1/Lotgi1.home.html webcite database and organism names that we collected are listed and categorized according to gene group. The EDV29271 Trichoplax adhaerens Zic amino acid sequence was manually added from the genome database, and indicates as "EDV29271+edit". The inset in right bottom indicates the numbers of non-redundant sequences in each class.

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Additional file 3:

PHI-BLAST pattern validity. Percentage occurrence of the PHI-BLAST pattern in the tCWCH2 library (A). Most frequent amino acid sequence for tCWCH2 in the PHI-BLAST result. A loose search pattern increases the number of BLAST hits, and increases the percentages of recovery of library (B). The tCWCH2 sequence motif collection contains 551 sequences from the NCBI protein database and 36 sequences from the NCBI nucleotide or other databases.

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Additional file 4:

The sequence of the conserved domains of Arid2 and Rsc9. The ARID domain (A) and the ZF domain (B) are conserved in Arid2 and Rsc9. Core amino acid residues of the ARID domain are indicated by asterisks (*) in (A). The structure of the tCWCH2 motifs and flanking sequence are shown in (B). Conserved sequence [IxL (S/T) AxL (I/V) L (K/R) N (I/L) x(K/R)] are indicated by asterisks (*). Hs, Homo sapiens; Dr, Danio rerio; Bm, Brugia malayi; Dm, Drosophila melanogaster; Nc Neurospora crassa; Spo, Schizosaccharomyces pombe.

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Additional file 5:

Zinc finger domains of Mizf. We found novel ZFs in Mizf. A pseudo ZF structure was found between ZF4 and ZF5 (indicated as ZF?). Hs, Homo sapiens; Dr, Danio rerio; Ta, Trichoplax adhaerens; Ci, Ciona intestinalis; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans.

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Additional file 6:

Sequence alignment of Zap1 and ZafA. Zinc homeostasis genes Zap1 and ZafA have structural similarity. Conservation of ZF8 was weak. Um, Ustilago maydis; Cn, Cryptococcus neoformans; Afu, Aspergillus fumigatus; Mg, Magnaporthe grisea; Yl, Yarrowia lipolytica; Ca, Candida albicans; Sc, Saccharomyces cerevisiae.

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Additional file 7:

Sequence alignment of zinc finger domain of Fungl, human GLI3, and Fungl-4ZF genes. We propose the common gene name, Fungl: Fungus Gli like. Afu, Aspergillus fumigatus; Nc, Neurospora crassa; Yl, Yarrowia lipolytica; Mgl, Malasszia globosa; Um, Ustilago maydis; Ro, Rhizopus oryzae; Ecu, Encephalitozoon cuniculi; Ca, Candida albicans; Lbi, Laccaria bicolor; Eb, Enterocytozoon bieneusi; Alo, Antonospora locustae; Cn, Cryptococcus neoformans; Hs, Homo sapiens; Bde, Batrachochytrium dendrobatidis.

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Additional file 8:

Sequence alignment of Twincl zinc finger domain. Based on its structural features, we named this gene family Twincl (Tandem CWCH2 protein C-terminal). Afu, Aspergillus fumigatus; Nf, Neosartorya fischeri; Cim, Coccidioides immitis; Pn, Phaeosphaeria nodorum; Gz, Gibberella zeae; Mgr, Magnaporthe grisea; Nc, Neurospora crassa.

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Additional file 9:

Sequence alignment of Clr1 zinc finger domain. Spo, Schizosaccharomyces pombe; Sj, Schizosaccharomyces japonicus; Cn, Cryptococcus neoformans.

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Additional file 10:

Sequence alignment of Monosiga, Dictyostelium, and plant gene. (A) Zinc finger domain alignment of Dictyostelium discoideum hypothetical protein (DdHp) and Monosiga brevicollis tCWCH2. DdHp2 contains two tCWCH2 domains {ZF12 (ZF1-ZF2) and ZF34 (ZF3-ZF4)}. (B) Plant REF6 Physcomitrella patens (XP_001771543) gene has tCWCH2 sequence. It has strong homology to Arabidopsis REF6 (NP_680116), Oryza sativa gene (NP_001045137) and Vitis vinifera (CAO64178) gene, but the tryptophan residue is not conserved in Arabidopsis and other plants. An alignment of zinc finger domain of these genes is shown. Amino acid identity between sequences is shown by a dot (.).

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Additional file 11:

Sequence alignment for phylogenic tree analysis. Conserved cysteine and histidine residues are indicated with an asterisk (*). Afr, Artemia franciscana; Afu, Aspergillus fumigatus; Aga, Anopheles gambiae; Alo, Antonospora locustae; Ape, Asterina pectinifera; Bde, Batrachochytrium dendrobatidis; Bfl, Branchiostoma floridae; Cin, Ciona intestinalis; Cn, Cryptococcus neoformans; Co, Corbicula sp.; Da, Dicyema acuticephalum; Dd, Dictyostelium discoideum; Dj, Dugesia japonica; Dm, Drosophila melanogaster; Hr, Halocynthia roretzi; Hs, Homo sapiens; Hv, Hydra vulgaris; Lbl, Loligo bleekeri; Mms, Mus musculus; Nf, Neosartorya fischeri; Nve, Nematostella vectensis; Oo, Octopus ocellatus; Pi, Pandinus imperator; Ro, Rhizopus oryzae; Sc, Saccharomyces cerevisiae; Sm, Schistosoma mansoni; Sp, Strongylocentrotus purpuratus; Sso, Spisula solidissima; Ssu, Scolionema suvaense; Ta, Trichoplax adhaerens; Tt, Tubifex tubifex; Um, Ustilago maydis; Xl, Xenopus laevis; Yl, Yarrowia lipolytica.

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Additional file 12:

BI tree of tCWCH2+1ZF. BI tree analysis was performed on 8 × 10⁶ generations using WAG model. Average standard deviation of split frequencies was lower than 0.001 at the end of the analysis. Abbreviations are the same as those in Additional file 11.

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Additional file 13:

ML tree of tCWCH2+1ZF. ML tree analysis was performed using WAG model with "empirical base frequencies", "maximum likelihood search", and "estimate proportion of invariable sites" options of RAxML [75]. 100 replicates were set for the bootstrap analysis. Abbreviations are the same as those in Additional file 11.

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Additional file 14:

NJ tree of tCWCH2+1ZF. NJ tree analysis was performed using JTT model and "pair wise deletion", "Rate among site = different (gamma distribution = 0.62)" options of MEGA4 (http://www.megasoftware.net/ webcite, [73,74]). The gamma distributions alpha parameter was calculated by "Tree-Puzzle" (http://www.tree-puzzle.de/ webcite, [72]). 1000 replicates were set for the bootstrap analysis. Abbreviations are the same as those in Additional file 11.

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